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Updated: Sep 19, 2026

Multipronged Phenotyping Approaches to Characterize Sugarcane Root Systems
Published on: August 17, 2022
Genome-wide association study for sucrose content and cane yield-related traits in sugarcane (Saccharum spp.) using
Md Sariful Islam1, Héctor Orozco2, José Quemé2
1Sugarcane Production Research Unit, USDA ARS SEA, Canal Point, 33438 FL USA.
Abstract:
Sugarcane breeding programs worldwide remain constrained by the limited availability of robust molecular markers for yield- and sugar-related traits. To address this limitation, we conducted a genome-wide association study (GWAS) using 397 globally diverse germplasm accessions. Phenotypic data for six yield and sugar traits were obtained from replicated trials at two locations in Guatemala. Genotyping was performed using genotyping-by-sequencing (GBS), and sequence reads were aligned to the polyploid sugarcane reference genome R570. GWAS analyses performed with GWASpoly identified 17, 44, and 93 unique SNPs significantly associated with four traits (stalk diameter, stalk height, stalk population, and stalk weight), five traits, and five traits in Playa Grande, San Vicente, and the combined dataset, respectively. Eleven SNPs exhibited consistent associations with stalk diameter, stalk population, and tons cane per hectare across both locations. Fourteen significant SNPs colocalized with 12 putative genes implicated in Brix, stalk diameter, stalk population, and tons cane per hectare. These results provide high-confidence loci and candidate genes that can advance the development of informative molecular markers to accelerate genetic improvement and cultivar development in sugarcane.
Supplementary Information:
The online version contains supplementary material available at https://doi.org/10.1007/s13205-026-05062-w.
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